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RNAinverse specifications

Information


Unique identifier OMICS_04759
Name RNAinverse
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline RNAinverse <>

RNAinverse in publications

 (12)
PMCID: 5123390
DOI: 10.1186/s12864-016-3105-4

[…] in the structures ensemble needed in order for it to be able to fulfill its function? equally for the rna design problem, most methods are based on local searches, from a random search as in rnainverse [] or with an ant algorithm as in antarna-ant []. the observed diversity in the quality of sequences at a minimal distance from each other demonstrates the need of more global tools, like […]

PMCID: 4752187
PMID: 26713687
DOI: 10.1089/cmb.2015.0179

[…] requires that all probes have the same length, then an additional process, , is run to extend these probes into ℓ-long unstructured probes. other methods may be used for this step, such as rnainverse (lorenz et al., ). the total set in the end is the complete set., if self-structured k-mers exist, the algorithm can be used to solve the two subproblems (see ). the algorithm as is solves […]

PMCID: 4559319
PMID: 26335276
DOI: 10.1186/s12859-015-0706-x

[…] which have the same number of non-dominated solutions) of modena is also different from that of frnakenstein., secondly, in the default setting of frnakenstein, rna sequences are initialized by rnainverse where a target structure is randomly selected from multiple targets. this initialization does not guarantee the compatibility with multiple target structures. modena initializes rna […]

PMCID: 4521916
PMID: 26230932
DOI: 10.1371/journal.pone.0134262

[…] approach to solve it by stochastic optimization relies on the solution of the direct problem [,]. initially, a seed sequence is chosen, after which a local search strategy was used in the original rnainverse of [] to mutate the seed and repeatedly perform rna folding prediction by energy minimization. recently, aside of many important contributions by several groups in the field of rna inverse […]

PMCID: 4333902
PMID: 25649229
DOI: 10.1186/s12864-014-1203-8

[…] $$ neutrality(s) > \frac{1}{100}\sum\limits_{i=1}^{100}neutrality(inv)_{i} $$ \end{document}neutrality(s)>1100∑i=1100neutrality(inv)i, for each sequence tested for robustness, rnainverse [] was used to generated 10 inverse folded sequences and each of those are used to seed 10 random walks resulting in a total of 100 inverse folded sequences for each s. input sequences […]


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RNAinverse institution(s)
Institute for Theoretical Chemistry, University of Vienna

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